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A paragraph from the highlights of "Transcriptomics: Throwing light on dark matter" by L. Flintoft (Nature Reviews Genetics 11, 455, 2010), says: "Reports over the past few years of extensive transcription throughout eukaryotic genomes have led to considerable excitement. However, doubts have been raised about the methods that have detected this pervasive(More)
The formulation of network models from global protein studies is essential to understand the functioning of organisms. Network models of the proteome enable the application of Complex Network Analysis, a quantitative framework to investigate large complex networks using techniques from graph theory, statistical physics, dynamical systems and other fields.(More)
do we need " networks " in systems medi-cine? Maybe there is not a simple answer. Until recently, scientists from mathematics, physics, statistics, machine learning, computer science, and similar quantitative/ computational disciplines were converging to bioinformatics for known reasons. A main one was to support the experimental and theoretical work of(More)
Typical high-abundant proteins, including albumin, IgG, IgA and others, are the target of depletion methods usually applied to two-dimensional electrophoresis (2DE) of human biological fluids like serum and plasma. Detection of low-abundant proteins is of interest with regard to biomarkers for disease when being studied by 2DE or liquid chromatography-mass(More)
This paper presents an application of the Independent Component Analysis (ICA) method to genomic data. In particular, experimentally produced perturbation effects over the E.coli bacterium are monitored through the changes of gene expression values observed at regular times, and until steady state has been reached. The aim is to control the response of the(More)
Retinoblastoma, a very aggressive cancer of the developing retina, initiatiates by the biallelic loss of RB1 gene, and progresses very quickly following RB1 inactivation. While its genome is stable, multiple pathways are deregulated, also epigenetically. After reviewing the main findings in relation with recently validated markers, we propose an integrative(More)
Epigenetic variation is a main regulation mechanism of gene expression in various cancer histotypes, and due to its reversibility, the potential impact in therapy can be very relevant. Based on a selected pair, breast cancer (BC) and melanoma, we conducted inference analysis in parallel on a few cell lines (MCF-7 for BC and A375 for melanoma). Starting from(More)